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annotate planemo/lib/python3.7/site-packages/cwltool/tests/test_singularity.py @ 0:d30785e31577 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:18:57 -0400
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d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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1 import sys
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2 import os
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3 import pytest
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4
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5 import distutils.spawn
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6
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7 import schema_salad.validate
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8
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9 from cwltool.main import main
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10
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11 from .util import (get_data, get_main_output, needs_singularity,
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12 needs_singularity_2_6, working_directory)
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13
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14 sys.argv = ['']
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15
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16
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17 @needs_singularity_2_6
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18 def test_singularity_pullfolder(tmp_path):
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19 workdir = tmp_path / "working_dir_new"
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20 workdir.mkdir()
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21 os.chdir(str(workdir))
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22 pullfolder = tmp_path / "pullfolder"
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23 pullfolder.mkdir()
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24 env = os.environ.copy()
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25 env["SINGULARITY_PULLFOLDER"] = str(pullfolder)
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26 result_code, stdout, stderr = get_main_output(
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27 ['--singularity', get_data("tests/sing_pullfolder_test.cwl"), "--message", "hello"], env=env)
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28 print(stdout)
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29 print(stderr)
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30 assert result_code == 0
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31 image = pullfolder/"debian.img"
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32 assert image.exists()
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33
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34 @needs_singularity
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35 def test_singularity_workflow(tmpdir):
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36 with working_directory(str(tmpdir)):
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37 error_code, _, stderr = get_main_output(
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38 ['--singularity', '--default-container', 'debian', '--debug',
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39 get_data("tests/wf/hello-workflow.cwl"), "--usermessage", "hello"])
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40 assert "completed success" in stderr, stderr
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41 assert error_code == 0
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42
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43 def test_singularity_iwdr():
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44 result_code = main(
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45 ['--singularity', '--default-container', 'debian',
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46 get_data("tests/wf/iwdr-entry.cwl"), "--message", "hello"])
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47 singularity_installed = bool(distutils.spawn.find_executable('singularity'))
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48 if singularity_installed:
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49 assert result_code == 0
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50 else:
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51 assert result_code != 0
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52
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53 @needs_singularity
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54 def test_singularity_incorrect_image_pull():
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55 result_code, _, stderr = get_main_output(
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56 ['--singularity', '--default-container', 'non-existant-weird-image',
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57 get_data("tests/wf/hello-workflow.cwl"), "--usermessage", "hello"])
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58 assert result_code != 0
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59
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60 @needs_singularity
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61 def test_singularity_local(tmp_path):
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62 workdir = tmp_path / "working_dir"
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63 workdir.mkdir()
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64 os.chdir(str(workdir))
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65 result_code, stdout, stderr = get_main_output(
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66 ['--singularity', get_data("tests/sing_pullfolder_test.cwl"), "--message", "hello"])
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67 assert result_code == 0
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68
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69 @needs_singularity_2_6
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70 def test_singularity_docker_image_id_in_tool(tmp_path):
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71 workdir = tmp_path / "working_dir"
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72 workdir.mkdir()
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73 os.chdir(str(workdir))
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74 result_code, stdout, stderr = get_main_output(
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75 ['--singularity', get_data("tests/sing_pullfolder_test.cwl"), "--message", "hello"])
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76 result_code1, stdout, stderr = get_main_output(
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77 ['--singularity', get_data("tests/debian_image_id.cwl"), "--message", "hello"])
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78 assert result_code1 == 0